Solution
In order to properly measure your signal set your BNC-2090A to be in the 'DIFF' configuration. BNC cables inherently transmit a differential pair of signals, so even though your probe terminates in a single BNC cable, that cable is transmitting two differential signals.
As shown in Figure 2-2 below, taken from the BNC-2090A's User Manual, by connecting a single BNC cable to AI 0 in the 'DIFF' configuration, the BNC-2090A will break out that BNC cable's differential pair into 2 signals and send one signal to AI 0 on the DAQ device and the other to AI 8 of the DAQ device. You are only connecting 1 BNC cable to the BNC-2090A but it will send 2 distinct signals to the DAQ device, complying with the differential input requirement.